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Is the genetic code a real code?

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A fierce argument has been raging over at Barry Arrington’s post, A dog is a chien is a perro is a hund, over whether the genetic code is really a semiotic code, or whether “code” is merely a scientific term of convenience in this case. In this post, I hope to clarify the issues and sharpen the discussion between the two sides.

Let’s begin with Barry Arrington’s argument:

An arrangement of signs is arbitrary when the identical purpose could be accomplished through a different arrangement of signs if the rules of the semiotic code were different…

Here’s an example of an arbitrary arrangement of signs: DOG. This is the arrangement of signs English speakers use when they intend to represent Canis lupus familiaris. … Now, the point is that there is nothing inherent in a dog that requires it to be represented in the English language with the letters “D” followed by “O” followed by “G.” If the rules of the semiotic code (i.e., the English language) were different, the identical purpose could be accomplished through a different arrangement of signs. We know this because in other codes the same purpose is accomplished with vastly different signs. In French the purpose is accomplished with the following arrangement of signs: C H I E N. In Spanish the purpose is accomplished with the following arrangement of signs: P E R R O. In German the purpose is accomplished with the following arrangement of signs: H U N D…

How does this apply to the DNA code? The arrangement of signs constituting a particular instruction in the DNA code is arbitrary in the same way that the arrangement of signs for representing Canis lupus familiaris is arbitrary. For example, suppose in a particular strand of DNA the arrangement “AGC” means “add amino acid X.” There is nothing about amino acid X that requires the instruction “add amino acid X” to be represented by “AGC.” …

Why is all of this important to ID? It is important because it shows that the DNA code is not analogous to a semiotic code. It is isometric with a semiotic code. In other words, the digital code embedded in DNA is not “like” a semiotic code, it “is” a semiotic code. This in turn is important because there is only one known source for a semiotic code: intelligent agency.

In what follows, I’d like to sort out some of the issues relating to whether we can properly speak of a genetic code, and whether talk of a “genetic code” is indispensable to biology. I’ll also look at some objections to the term “genetic code,” before drawing a conclusion as to how the issue might be successfully adjudicated on a scientific basis.

What is “the genetic code”?

Here is how Wikipedia defines the genetic code:

The genetic code is the set of rules by which information encoded within genetic material (DNA or mRNA sequences) is translated into proteins (amino acid sequences) by living cells. Biological decoding is accomplished by the ribosome, which links amino acids in an order specified by mRNA, using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms, and can be expressed in a simple table with 64 entries.

The code defines how sequences of these nucleotide triplets, called codons, specify which amino acid will be added next during protein synthesis. With some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. Because the vast majority of genes are encoded with exactly the same code (see the RNA codon table), this particular code is often referred to as the canonical or standard genetic code, or simply the genetic code, though in fact some variant codes have evolved. For example, protein synthesis in human mitochondria relies on a genetic code that differs from the standard genetic code.

Is the genetic code just a metaphor, or is it real?

On May 2, 2011, Professor Gregory Chaitin, a world-famous mathematician and computer scientist, gave a talk entitled, Life as Evolving Software. The talk was given at PPGC UFRGS (Portal do Programa de Pos-Graduacao em Computacao da Universidade Federal do Rio Grande do Sul Mestrado), in Brazil. Professor Chaitin is an avowed neo-Darwinist who is currently endeavoring to create a new mathematical version of Darwin’s theory which rigorously proves that evolution can really work. In 2012, Professor Chaitin published a book entitled, Proving Darwin: Making Biology Mathematical (Pantheon, ISBN: 978-0-375-42314-7). Here are some short excerpts from what Professor Chaitin said about the software of life in his talk in May 2011:

[P]eople often talk about DNA as a kind of programming language, and they mean it sort of loosely, as some kind of metaphor, and we all know about that metaphor. It’s especially used a lot, I think, in evo-devo. But it’s a very natural metaphor, because there are lots of analogies. For example, people talk about computer viruses. And another analogy is: there is this sort of principle in biology as well as in the software world that you don’t start over. If you have a very large software project, and it’s years old, then the software tends to get complicated. You start having the whole history of the software project in the software, because you can’t start over… You … can try adding new stuff on top…

So the point is that now there is a well-known analogy between the software in the natural world and the software that we create in technology. But what I’m saying is, it’s not just an analogy. You can actually take advantage of that, to develop a mathematical theory of biology, at some fundamental level…

Here’s basically the idea. We all know about computer programming languages, and they’re relatively recent, right? Fifty or sixty years, maybe, I don’t know. So … this is artificial digital software – artificial because it’s man-made: we came up with it. Now there is natural digital software, meanwhile, … by which I mean DNA, and this is much, much older – three or four billion years. And the interesting thing about this software is that it’s been there all along, in every cell, in every living being on this planet, except that we didn’t realize that … there was software there until we invented software on our own, and after that, we could see that we were surrounded by software…

So this is the main idea, I think: I’m sort of postulating that DNA is a universal programming language. I see no reason to suppose that it’s less powerful than that. So it’s sort of a shocking thing that we have this very very old software around…

So here’s the way I’m looking at biology now, in this viewpoint. Life is evolving software. Bodies are unimportant, right? The hardware is unimportant. The software is important…

In the opinion of this eminent Darwinist scientist, then, talk of a genetic code is quite literal: “it’s not just an analogy.”

Is the information in life quantifiable?

Some ID critics object that the functional complex specified information we see in living things is unquantifiable. However, this criticism can be easily rebutted. The term “functional information” has been rigorously defined by Szostak and his colleagues in recent scientific papers:

1. Hazen, R.M.; Griffin, P.L.; Carothers, J.M.; Szostak, J.W. 2007, Functional information and the emergence of biocomplexity, Proc Natl Acad Sci U S A, 104 Suppl 1, 8574-81.

2. Szostak, J.W. 2003, Functional information: Molecular messages, Nature, 423, (6941) 689.

3. Carothers, J.M.; Oestreich, S.C.; Davis, J.H.; Szostak, J.W. 2004, Informational complexity and functional activity of RNA structures, J Am Chem Soc, 126, (16) 5130-7.

For instance, here is how Hazen, Carothers and Szostak define functional information in the abstract of their 2007 paper:

Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define “functional information,” I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA–GTP binding energy), I(Ex) = -log2[F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function [greater than or equal to] Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree.

The information in a protein is therefore quantifiable, and has been quantified, as those who are familiar with Dr. Douglas Axe’s work will be aware.

Do we have to speak of a “genetic code”?

On Barry Arrington’s post, A dog is a chien is a perro is a hund, ID critic Alan Fox has proposed that talk of a “genetic code,” while convenient for scientific purposes, is ultimately reducible to chemistry:

Interactions between molecules involve their chemical properties; charge, conformation, level of hydrophilic and lipophilic residues etc. Nothing analogous to language goes on here. (Comment 118)

DNA sequences translate to specific protein sequences by chemical interactions. (Comment 174)

I see no communicative element in the chemical processes that occur when DNA sequences are transcribed into RNA and translated into polypeptide sequences. It’s all a result of the inherent physical and chemical properties of the interacting molecules… To lump chemical processes in with aspects of linguistics is such a stretch that any set that encompasses both is large enough and fuzzy enough to be meaningless… At the cellular and sub-cellular level and consequently and cumulatively at the level of the organism there is a huge amount of communication going on. It is chemical communication… “Encode” could be used as a defined shorthand for some step in the chemical processes that go on in the cell, of course. Maybe there is a scientific definition in the context of biochemistry. (Comment 184)

DNA transcription and translation is a chemical chain of reactions that depends on the spacial conformation and inherent chemical properties of atoms and molecules. (Comment 274)

Eric Anderson challenged Alan Fox at one point in the exchange of opinions:

I hope you aren’t saying that specific protein sequences arise automatically by chemical reactions once the sequence of nucleotides is exposed? There is a whole system in place that takes the 4-character digital code and translates it on the basis of the genetic code into a subsequent physical chain of amino acids. This does not just happen by chemistry. The translation (and it is not just called that by analogy, it is really what is going on) is precisely one of the things that highlights the semiotic nature of the system we are dealing with. (Comment 179)

In a similar vein, Joe responded:

Except there isn’t any physical and chemical properties that DETERMINE which codon REPRESENTS what amino acid. (Comment 192)

Without being uncharitable to Alan Fox, I’d like to get to what seems to me to be the fundamental issue dividing those who insist that talk of a “genetic code” is indispensable to biology from those who say it is not. The critical question, it seems to me, is whether life can be described and explained from the bottom up. What Fox is saying is that we can give from reductionist, bottom-up account which has the same explanatory power as talk of a genetic code. The latter might be more convenient than the former, but is is no more powerful.

If it turns out, then, that the genetic code is a top-down feature of life, then it will indeed be indispensable to biology. But is it? To answer this question, we need to examine the various hypotheses regarding the origin of the genetic code.

Hypotheses regarding the origin of the code

I’d like to quote again from the Wikipedia article on the genetic code, as no-one will accuse Wikipedia of being based in favor of Intelligent Design:

If amino acids were randomly assigned to triplet codons, then there would be 1.5 x 10^84 possible genetic codes to choose from. However, the genetic code used by all known forms of life is nearly universal with few minor variations. This suggests that a single evolutionary history underlies the origin of the genetic code. Many hypotheses on the evolutionary origins of the universal genetic code have been proposed.

Four themes run through the many hypotheses about the evolution of the genetic code:

* Chemical principles govern specific RNA interaction with amino acids. Experiments with aptamers showed that some amino acids have a selective chemical affinity for the base triplets that code for them. Recent experiments show that of the 8 amino acids tested, 6 show some RNA triplet-amino acid association.

* Biosynthetic expansion. The standard modern genetic code grew from a simpler earlier code through a process of “biosynthetic expansion”. Here the idea is that primordial life “discovered” new amino acids (for example, as by-products of metabolism) and later incorporated some of these into the machinery of genetic coding. Although much circumstantial evidence has been found to suggest that fewer different amino acids were used in the past than today, precise and detailed hypotheses about which amino acids entered the code in what order have proved far more controversial.

* Natural selection has led to codon assignments of the genetic code that minimize the effects of mutations. A recent hypothesis suggests that the triplet code was derived from codes that used longer than triplet codons (such as quadruplet codons). Longer than triplet decoding would have higher degree of codon redundancy and would be more error resistant than the triplet decoding. This feature could allow accurate decoding in the absence of highly complex translational machinery such as the ribosome and before cells began making ribosomes.

* Information channels: Information-theoretic approaches model the process of translating the genetic code into corresponding amino acids as an error-prone information channel. The inherent noise (that is, the error) in the channel poses the organism with a fundamental question: how can a genetic code be constructed to withstand the impact of noise while accurately and efficiently translating information? These “rate-distortion” models suggest that the genetic code originated as a result of the interplay of the three conflicting evolutionary forces: the needs for diverse amino-acids, for error-tolerance and for minimal cost of resources. The code emerges at a coding transition when the mapping of codons to amino-acids becomes nonrandom. The emergence of the code is governed by the topology defined by the probable errors and is related to the map coloring problem.

Transfer RNA molecules appear to have evolved before modern aminoacyl-tRNA synthetases, so the latter cannot be part of the explanation of its patterns.

There are enough data to refute the possibility that the genetic code was randomly constructed (“a frozen accident”). For example, the genetic code clusters certain amino acid assignments. Amino acids that share the same biosynthetic pathway tend to have the same first base in their codons. Amino acids with similar physical properties tend to have similar codons. A robust hypothesis for the origin of genetic code should also address or predict the following gross features of the codon table:

1. absence of codons for D-amino acids

2. secondary codon patterns for some amino acids

3. confinement of synonymous positions to third position

4. limitation to 20 amino acids instead of a number closer to 64

5. relation of stop codon patterns to amino acid coding patterns

It seems to me that what the “code skeptics” are saying is that if we can account for the origin of the genetic code in terms of either bottom-up processes (e.g. unknown chemical principles that make the code a necessity), or bottom-up constraints (i.e. a kind of selection process that occurred early in the evolution of life, and that favored the code we have now), then we can dispense with the code metaphor. The ultimate explanation for the code has nothing to do with choice or agency; it is ultimately the product of necessity.

In responding to the “code skeptics,” we need to keep in mind that they are bound by their own methodology to explain the origin of the genetic code in non-teleological, causal terms. They need to explain how things happened in the way that they suppose. Thus if a code-skeptic were to argue that living things have the code they do because it is one which accurately and efficiently translates information in a way that withstands the impact of noise, then he/she is illicitly substituting a teleological explanation for an efficient causal one. We need to ask the skeptic: how did Nature arrive at such an ideal code as the one we find in living things today?

By contrast, a “top-down” explanation of life goes beyond such reductionistic accounts. On a top-down account, it makes perfect sense to say that the genetic code has the properties it has because they help it to withstand the impact of noise while accurately and efficiently translating information. The “because” here is a teleological one. A teleological explanation like this ties in perfectly well with intelligent agency: normally the question we ask an agent when they do something is: “Why did you do it that way?” The question of how the agent did it is of secondary importance, and it may be the case that if the agent is a very intelligent one, we might not even understand his/her “How” explanation. But we would still want to know “Why?” And in the case of the genetic code, we have an answer to that question.

We currently lack even a plausible natural process which could have generated the genetic code. On the other hand, we know that intelligent agents can generate codes. The default hypothesis should therefore be that the code we find in living things is the product of an Intelligent Agent.

The question we now have to ask ourselves is whether a teleological account of life implies an Intelligent Designer. Recently, the philosopher Thomas Nagel has argued for a form of teleological naturalism, which I discussed in a recent post. Teleological naturalism at least recognizes the inadequacy of non-purposive causal explanations of the cosmos. That’s a big step in the right direction, and I respect Thomas Nagel for taking that step. Nevertheless, it has a fatal flaw: Nature, being unintelligent, does not and cannot look forward. It is precisely for this reason that the Intelligent Design movement contends that if the genetic code can only be understood from a top-down teleological perspective, then the emergence of the genetic code can only be adequately explained in terms of a Mind which produced it.

Does talk of a “genetic code” beg the question, by assuming the existence of a conscious sender and receiver and a rule-maker?

On Barry Arrington’s post, A dog is a chien is a perro is a hund, Alan Fox objected to talk of a “genetic code” on the grounds that “there is no giver or receiver of information in a communicative sense” (comment 274). He also objected to “rule” terminology on the grounds that it begs the question of the existence of a rule-maker. However, Chance Ratcliff successfully rebutted this objection when he defined the rule using the mathematical notion of a mapping: “the DNA to polypeptide mapping function is in the form F:A→B, where F: is performed essentially by RNA polymerase, aminoacyl trna synthetase, and the ribosome, and works by mechanism to convert elements of A (codons) into elements of B (amino acids)” (comment 308).

Likewise, there is no reason why we cannot speak of a molecule as a sender or receiver of information.

The road ahead

The Wikipedia article on the genetic code mentions five striking facts about the genetic code which any successful account must be able to explain. It seems to me that Intelligent Design would do well to focus on these “nitty-gritty” questions, in order to demonstrate its scientific superiority to “bottom-up,” reductionistic accounts of life. That, for the time being, is the way forward, I believe. If ID proponents can explain a lot more about the peculiar properties of life than their Darwinian counterparts, then the younger generation of scientists, who are not wedded to old dogmas and fossilized ways of thinking, will start to take notice.

What do readers think?

Comments
There's more to matter than just matter. :)Mung
February 19, 2013
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Box @65:
I’m arguing that each organism is an agent on its own – and not just ordered matter and energy, as Stephen Meyer seems to think.
I agree with you that the question of individual agency is a most interesting question. We could debate for hours, no doubt, about whether "each organism" has agency -- each animal, plant, amoeba, etc. But let's focus on humans for a moment as an example. Does human agency arise from the human's composition, from the cells and machines that make up the human? In other words, is our agency (and consciousness, which is closely related) an emergent property of our material makeup? I don't think ID is directly relevant to this question, as interesting as the question is. Most Christians, as well as many other faiths, would argue that there is something more to us than just our material makeup -- say, a spirit, or a soul, or an intelligence, or something that goes beyond the physical and the material. But again, they would say so on the basis of their religious/philosophical position, not on the basis of ID. No prominent ID opponent I am aware of takes the position that we are only matter and energy. And your quotes from Meyer certainly don't state that, so you are misrepresenting his position. Further, prominent ID proponents all agree that humans do have individual agency. Indeed, our experience with human agency is the primary avenue through which we can understand, and analogize, and interpret the fact that there is a broader agency at work in the creation of biological systems. I don't mean to be rude and I hope you will take this in a lighthearted spirit, but I have to say it seems that you are itching to pick a fight but don't have an opponent. So you are grasping at a sentence here or a quote there to try and turn some of the prominent ID proponents (like Meyer, in this instance) into opponents on this issue. But ID does not speak to the question of whether every organism has agency. Furthermore, every prominent ID proponent agrees that humans have individual agency. So you are waging a battle over a non-existent dispute. Tilting at windmills as it were . . .Eric Anderson
February 19, 2013
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Hello aham, The central point of the argument, particularly the semiotic argument, is that the genetic code operates in exactly the same manner as any other form of recorded information. The material conditions are identical.Upright BiPed
February 19, 2013
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I should apologise in advance for my poor English and a great number of errors, English is not my native language.aham
February 19, 2013
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I didn't realise that ID requires a HE who designed. What if it is Them or even Us or something that we can't even imagine? As for the DNA being a code, it certainly appears to be so and carry the function of. However, it may also not work in a same way as codes we use, so to say a linear set of instructions. It may be more like a music notation 'code'. Take a symphony. Play each instrument individually in linear manner. Are you following a 'code', well yes, a set of instructions recorded in a form of stave notation, a melody is produced as a result. But its nonsense, the information is only truly understood if it is read at the same time. In mathematics this is also can be demonstrated, its the same in physics etc. Simultaneous function of the entire existence is a vary delicate thing. Maybe we ought to remember that?aham
February 19, 2013
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Semi-OT: This video on the bacterial flagellum will have elements that are familiar to many, but gets into some details about the construction process, which is no less remarkable than the structures themselves. Biological videophiles should find this entertaining.Chance Ratcliff
February 18, 2013
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@Eric Anderson (60) I'm aware that ID requires one intelligent agent - the master designer. But this master programmer is external to the life he creates. I'm arguing that each organism is an agent on its own - and not just ordered matter and energy, as Stephen Meyer seems to think.Box
February 18, 2013
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Box: I think we are simply looking at different things and problems. In that light, I am interested in the question of credibly knowing on observable evidence THAT design was or was not credible as causal process. Whodunit is a different issue and not accessible from what we have in hand to address on the material issue. KFkairosfocus
February 18, 2013
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The visualizations around 7:50 from the above linked Drew Berry video are stunning.Chance Ratcliff
February 18, 2013
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Box,
"However the impression still remains that the ID movement puts too much emphasis on the mechanical aspect of life. Typing these words has a distinct machine-like aspect, but that is not the core of what is happening. The true miracle of life is agency and not the mechanical aspect."
I have to disagree. It's exactly the mechanical aspects which allow us to infer design from its physical effects. Without the explicit engineering of these nanotechnological wonders, we wouldn't be able to call out specified and irreducible complexity. Viewing the cell as a marvel of technological engineering follows from the biological design inference, which is the application of ID methods. Here is Drew Berry with another slew of what I believe to be the world's premier biological animations. The material is mind blowing, particularly at 5:00 and on (for the newer material). BTW "The Machine Metaphor" is certainly not applicable to life as a whole, but it's hard to deny that the constituents of life's physical elements are rooted in computational and mechanical realities. The concept of simple, cellular protoplasm has been replaced with the coordinated interplay of countless, purposefully designed parts - motors, signalling systems, transport systems, etc. ATP Synthase's mechanical nature is undeniable, as well as its brilliance, and it is the workhorse producer of the cell's energy currency.Chance Ratcliff
February 18, 2013
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#60 Indeed.Upright BiPed
February 18, 2013
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Box: The whole ID enterprise is about the fact that an agency is required. You know, the "intelligent" part of the "intelligent design" term. The mechanical part -- the machinery -- is interesting both because it is a work of engineering art, and because it points to the need for an intelligent agent. Your quote from Meyer is instructive as an example. You highlighted part of the quote, but forgot to bold the last clause -- the one about the master programmer. It seems you have read all the individual words but not understood the broader substance of his argument. You may rest quite assured that there is no risk the major ID proponents are only focused on the physical and the material. Every discussion, even those discussions focusing heavily on the mechanical structures, is underscored by the larger concept that these things don't just come about by purely physical and material processes -- they require an intelligent agency.Eric Anderson
February 18, 2013
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@Kairosfocus (57) Agency – the whole- plays a minor role in your writings. Although you do quote Michael Denton – who clearly expresses awareness of the big mystery of life’s wholeness – saying: “We would wonder at the level of control implicit in the movement of so many objects down so many seemingly endless conduits, all in perfect unison.“ And: “Unlike our own pseudo-automated assembly plants, where external controls are being continually applied, the cell's manufacturing capability is entirely self-regulated . . . . “ But when we get to Stephen Meyer the focus on agency is totally gone. Life is reduced to matter, energy and information – information rich macromolecules . You summarize Meyer’s ideas like this: "The universe is comprised of matter, energy, and the information that gives order [[better: functional organisation] to matter and energy, thereby bringing life into being. In the cell, information is carried by DNA, which functions like a software program. The signature in the cell is that of the master programmer of life." Is there no room for consciousness in the universe?
Kairosfocus (57)“In the ribosome, the anticodon fits, key-lock style to the mRNA’s active codon, and then the tRNA serves as a position-arm device with a loaded tool-tip. It then clicks the AA to the waiting AA-chain and exits the ribosome. These are machines, carrying out machine level things using molecular nanotech. This is not the level where agency as such arises. The smarts involved lie in the organization and the information-rich coordination.
Where is the acknowledgement of the active whole in your text? Everything that happens in the cell, including the actions of the ribosome, is subordinate to the whole – agency. That is the ultimate mystery of life. There is no level where the whole –agency- is not involved, because there is no level where things can operate uncoordinated. Michael Behe: “The essence of life is regulation: The cell controls how much and what kinds of chemicals it makes; when it loses control, it dies.”Box
February 18, 2013
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@Eric Anderson (56) Point taken. However the impression still remains that the ID movement puts too much emphasis on the mechanical aspect of life. Typing these words has a distinct machine-like aspect, but that is not the core of what is happening. The true miracle of life is agency and not the mechanical aspect.Box
February 18, 2013
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Box: Pardon, but no. I am speaking of machines within the cell, and their use of machine code because that is what I am seeing, things that are astonishingly familiar to -- but at once far more advanced [self replicating, self maintaining automata using molecular naotech!] than and using significantly different architectures -- technologies I work with. It is not that I want to go to a design inference so I look with the proverbial eye of faith, but that I see the machines and co-ordinated information controlled behaviour that I am so familiar with and am astonished. Maybe, it will help to hear my favourite definition of computer architecture: the assembly language [--> Machine code rendered human-readable] view of the computer. As to the case structure I pointed out, I am simply saying that the first structure in programming is the sequence of instructions s1s2s3 . . . In that context, we have an implicit table of instructions [way back, I used just such a table to hand code in machine language for 8-bit microcontroller systems] that the machine is looking for, and in case of sx from the set of possible instructions, it takes up a fetch, decode, execute cycle then proceeds to the next. The way proteins are assembled is that by the time we have mRNA in a ribosome to synthesise a protein, we have just such a sequence structure in a control tape: START - s2-s3 . . . sn -- STOP For each sx, there is a corresponding tRNA loaded with a specified AA, and which is then clicked onto the chain of AA's. There is a ratcheting forward, and the process continues. Until STOP. This is an algorithmic, step by step finite process that achieves a task. As has been pointed out the tRNA's are loaded separately with AA's by appropriate enzymes, and they carry the AA's on a universal CCA tool tip. This tip is at the opposite end of the folded tRNA from the anticodon. (It has been demonstrated that tRNA's can be reloaded with different AA's, they are inherently reprogrammable, i.e this is not a mechanically forced outcome.) In the ribosome, the anticodon fits, key-lock style to the mRNA's active codon, and then the tRNA serves as a position-arm device with a loaded tool-tip. It then clicks the AA to the waiting AA-chain and exits the ribosome. These are machines, carrying out machine level things using molecular nanotech. This is not the level where agency as such arises. The smarts involved lie in the organisation and the information-rich co-ordination. Life is not simply a machine, but life uses molecular nanotech machines at cellular level. The chemistry is familiar,t he physics is familiar, and these can be carried out in a test tube or the equivalent. For that matter, DNA has been coded with information in English. Why not read and watch here on? KFkairosfocus
February 18, 2013
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Box @54:
. . . let’s not forget that life isn’t a machine.
If you mean that life is not only a machine, then fair enough. But it is certainly instructive to consider life's machines. Living systems are clearly made up of machines that can be constructed, reverse-engineered, studied and appreciated. We cannot fully understand (or appreciate) life without understanding the machines that make up living systems.Eric Anderson
February 17, 2013
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JGuy @43 and 44: You bring up an excellent issue. Maybe I can rephrase it this way: If we have an instruction set that selects physical items, where the physical items either pre-exist or automatically come about through purely natural and material processes, does that instruction set constitute a code? A couple of thoughts: First, the instruction set would be written in some kind of language. A language is not a physical reality, but is always representative of some reality. So if we have a comprehensible string of representations that either mean something or do something, then in that sense we have a code. Now, we may not think of every language as a code, but in a very real sense that is what a language is: a set of representations that the users, by convention, agree represent certain things. Second, I'm trying to imagine in my mind's eye how an instruction set could possibly "select" physical items without some kind of translation process or other implementing program. Let's take the simplest possible example (which is akin to your hypothetical protein process): say, an instruction set that selects specifically colored blocks from a pile of blocks and puts them in order. Is the instruction set a code? Well, perhaps, in the sense that I've outlined above. But there is an additional way in which we may be dealing with code(s). How are the blocks selected? Well, there has to be some kind of mechnical structure, a machine with an arm, for example, that selects the blocks. And the process of taking an instruction from the instruction set, recognizing the instruction, translating that non-material instruction into a material process involving matter and energy (in this case seeking out, recognizing, moving the arm to grab the block, and moving the block to the appropriate location in the sequence of blocks) is, by definition, a translation of the instruction from the storage medium in which it was writtgn into a physical reality outside of the storage medium. Thus we see that it is impossible to have a DNA sequence that self-executes. There must be an interpretive/translative process. And this is completely ignoring for a moment the fact that there is a whole parallel process going on to link the amino acids to their receptors. And of course this also ignores the larger context which includes transport, review, repair, folding, and other processes. None of this just happens by chemistry. In summary, we have multiple levels of "code" or "language" active in the process of protein synthesis. In several of the instances we clearly have a mapping from one arbitrary character set onto another arbitrary character set (nucleotides to amino acids, for example), which underscores the semiotic aspect of the system in the cell. I'll leave it to UB to discuss whether he thinks an instruction set selecting from pre-existing items is also an instance of semiosis.Eric Anderson
February 17, 2013
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@Kairosfocus (52) I know what you are getting at. The thing is however, and I’m sure you agree, that there is a huge difference between machine and agency. This difference is being ignored when you equate case-structures, algorithms, computer code and such with life – like you did in post 52. I understand why you do it; you want to make an argument for intelligent design. For debate strategic purposes you descent to the same level of Darwinists - and agree on a purely mechanistic view on life – in order to drive your point home: it is intelligently designed. My point is: let’s not forget that life isn’t a machine. Stephen L. Talbott: “When a single protein can combine with several hundred different modifier molecules, leading to practically infinite combinatorial possibilities, and when that protein itself is an infinitesimal point in the vast, turbulent molecular sea of continual exchange that is the cell, and when the cell is one instance of maybe 100 trillion cells of some 250 different major types in the human body, from muscle to bone, from liver to brain, from blood to retina — well, it’s understandable that many researchers prefer not to stare too long at the larger picture. Nevertheless, we should keep in mind that the collaborative process mentioned above involves not just one table with “negotiators” gathered around it, but countless tables with countless participants and with messages flying back and forth in countless patterns as countless “decisions” are made in a manner somehow subordinated to the unity and multidimensioned interests of the organism as a whole. “Box
February 17, 2013
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BA: interesting. Will follow up further. KFkairosfocus
February 17, 2013
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Box: The meaning of machine code is built in by its designers, who in effect implement a case structure. On case code X, do action A, in a fetch, decode execute loop. This is given effect through co-ordinated executing machines. The machines that store, transfer, detect case and carry out pre-programmed operations are simply carrying out pre-programmed steps blindly, the smarts lie elsewhere, in the co-ordination that makes these steps in that order on a given machine having particular architecture do something useful. That is, algorithms, data structures, execution units etc all point beyond themselves to a source of the purposeful sequence of actions that are carried out. That is why this is so sensitive an issue for design objectors, as it is very hard indeed to dismiss that sort of context once we see such in action. And, observe how they are utterly at a loss to come up with cases where blind chance and mechanical necessity are observed to achieve this sort of thing. No great surprise, really; given what has been worked out for the 500 bit FSCO/I threshold. KFkairosfocus
February 17, 2013
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@Kairosfocus (49) The text I have written, which you are reading right now, is on its own pure matter. Its origin cannot be explained without agency but now it is pure matter nevertheless. The question is: how can it contain meaning? The only reason it has meaning right now is because you are reading it. Because your mind is adding meaning to this text. So, besides its origin, meaning needs a mind for its (continued) existence. - BTW this reminds me of quantum mechanic states which need a mind to become actualized. The same premise (needing a mind) does not go for e.g. computer code in my opinion. The difference is that we can walk away - thanks to the computer it functions independent from our minds.Box
February 17, 2013
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kairosfocus, A favor please? This guy has been putting out a series of, what I consider, excellent videos that have been well researched: micro-RNA and Non-Falsifiable Phylogenetic Trees - video http://www.youtube.com/watch?v=qv-i4pY6_MU&list=PL22eQqszdBpA7pUorVxj3GHhn7gugSY8x kf, I was wondering if you would be interested in featuring one, or perhaps a few, of this man's videos on its own blog entry on UD?,, I think the careful work he has done making these informative, fun to watch, videos merits any increased recognition UD may be able to give him.bornagain77
February 17, 2013
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Box: While I wait, UB is speaking about how such codes in the material world are instantiated, transmitted etc using material (and by expression, energy) expressions based on conventional -- thus arbitrary -- forms. There is no reason why something like a shepherd's crook standing up with a short cross bar should represent a sound made by putting lower lip under teeth and blowing with the mouth slightly open "ffff . . . " and there is no reason that his should be a part of a sound pattern that means say a certain annoying insect, a fly; for which other forms are used in other languages. And for that matter, fly means different things in different contexts, e.g. in a certain kind of angling, it means a combination of feathers, hairs, thread etc on a hook that represents a small fish sufficiently to attract a fish to the hook; i.e. a streamer fly. (And that too speaks of how the fish is sensing and responding to patterns that it interprets or its programming interprets as food on the fin trying to get away.) Ink scratches on paper that represent the sounds and words of English are a classic case, ASCII code that does the same is another, and DNA's genetic code is yet another. KFkairosfocus
February 17, 2013
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@Kairosfocus (46)
Kairosfocus: when I type this message, the materials and forces of nature constrain but do not determine the sequence of keys pressed.
Indeed. ‘Sequencing’ and ‘forming’ are good descriptive terms I my opinion. We as agents, as wholes, are living contexts navigating a sea of meaning.
Kairosfocus: Indeed, the first fact we each experience, is of being a conscious, purposeful, choosing, self-moved person. All other facts we become aware of and reflect upon are brought to us through that first fact. Those who undermine it, therefore refute themselves by reduction to self referential absurdity.
I fully agree. Agency breaches clearly and undeniably the principle of physical causal closure.
Kairosfocus: (..) a code known as written English. That code is not written in the laws and forces of nature, it is a matter of a cumulative choice of English speaking peoples over centuries. Whether we say red or rojo or whatever is not materially determined.
So the code is not materially determined because it is the cumulative choice of English speaking agencies. This I find a clear and persuasive argument. I’m not sure however if this corresponds exactly with what UB is saying.Box
February 17, 2013
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JG: The key problem for suggested deterministic models, is that the AA is attached to the tRNA that couples to the codon, through a universal CCA coupler, based on the action of a particular enzyme that serves as loader [notice the chicken-egg cycle involved!]. Indeed, tRNA's are capable of being re-programmed, as has been done in the lab. The link is INFORMATIONAL, not merely mechanical necessity. KFkairosfocus
February 17, 2013
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Box: engineering is defined as using the materials and forces of nature, intelligently, to design and create things for the benefit of man. Just so, when I type this message, the materials and forces of nature constrain but do not determine the sequence of keys pressed. I choose, and in choosing, I also choose to follow rules and symbols connected to the English language, y no Espanol. The tendency to reduce cause-effect dynamics to material, efficient causes leads to self-referential absurdities by undermining mind and its ability to choose to act rationally. Indeed, the first fact we each experience, is of being a conscious, purposeful, choosing, self-moved person. All other facts we become aware of and reflect upon are brought to us through that first fact. Those who undermine it, therefore refute themselves by reduction to self referential absurdity. In this broad context, we notice that the meaning of the glyphs strung together in this post is assigned by convention, by a code known as written English. That code is not written in the laws and forces of nature, it is a matter of a cumulative choice of English speaking peoples over centuries. Whether we say red or rojo or whatever is not materially determined. KFkairosfocus
February 17, 2013
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@Upright BiPed
Upright BiPed: An arbitrary relationship is a fundamental requirement in the operation of any system that produces physical effects from information, as opposed to physical law.
Are you stating that information breaches the principle of physical causal closure? So, besides obeying to physical law, matter obeys to information?
Upright BiPed: [consider]any concrete physical event not determined by inexorable physical law (… when an ant should attack it enemies ..) and then try to devise a system to bring that about by physical law alone. They will find that a context specific (non-physically determined) relationship is a physical requirement.
Are you stating that a context specific relationship is by definition non-physical? Are you confining physical law to the inner parts of the ant? So if context is involved in order to explain its behavior it follows a ‘non-physical’ explanation?Box
February 17, 2013
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p.s. Suppose that we found some physical or chemical pathway whereby you could apply several different influence, each of the same kind, to the initial steps of the pathway and get different results in the product. So, suppose there were 20 different initial influences we found that would give 20 different results form that process. Then suppose we engineered around this fortuitous process a useful system of encoding. Would then that original deterministic process be imputed with the essense of being a real code because of the mere fact that it was used as one? Guess in a way I'm just asking the same thing all over again :-/ JGuyJGuy
February 17, 2013
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UB @ 41 Thanks for the thought out response. I think I got it. As mentioned, I think I smuggled in the arbitrary aspect in my hypothetical when emphasizing the greater context. That is, the arbitrary stuff would then have been smuggled into the overall process as the DNA coded information, even if the genetic code would have been hypothetically determined by physical laws, there would have been an arbitrary element mixed in there. In that scenario, the DNA code would simply follow whatever different pattern determined by the "deterministic code" to make the same protein from the actual/real model. See if you can help me make sense of this a bit more though. The real world model is this: DNA code -> mRNA -> Ribosome (arbitrary Genetic Code) -> Protein. Hypothetical model: DNA code -> mRNA -> Ribosome (chemically determined Genetic Code(?)) -> Protein. In the hypothetical, to achieve the same target protein, the DNA code would simply have to be different to match the non-arbitrary code. So, my question was, is the Genetic Code not a code in the hypothetical model? My answer to myself was, yeah, it would still be. But I'm open to correction on that. But even if it would not be, at least there would be a real code in the hypothetical in the form of the DNA code. That is, it would be comprised of arbitrary sequences of information, that "mean" certain proteins. So, the hypothetical has either one or two real codes, but not zero. The real world model has at least two codes. The DNA Code (for proteins), and the Genetic Code (for amino acids). JGuyJGuy
February 17, 2013
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UB: Thank you for your kind words. I think you've done an excellent job in numerous posts of articulating some of the most fundamental issues. -----
An arbitrary relationship is a fundamental requirement in the operation of any system that produces physical effects from information, as opposed to physical law.
Exactly. In fact the ability of a physical medium to hold information is inversely proportional to the law-like structure of that medium.Eric Anderson
February 16, 2013
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